It's kinda funny that the greatest weapons technology supplier in the world and inventor of the Iron Man suit has no defense mechanisms at his house that would shoot down armed helicopters.

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The helicopters are posing as News choppers

Stark probably thought they were paparazzi

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This scene actually reminds me of the scene where Gary Busey shoots Danny Glover's former friend and source from a helicopter in Lethal Weapon, written by Shane Black. Admittedly, it wouldn't have occurred to me but for the Black connection.

Does he have a pemit for the suit? Its more lethal then a tank and people cannot own tanks and use them.

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Actually, you can own a tank and use it, provided you fill out the paperwork and pass a few tests and background checks. If I recall correctly, in one state, the difference between a permit for tank that has it's muzzle de-bored and a live-fire muzzle is around $50.

So who's in the Iron Man suit when it grabs Potts when she's in bed with Stark and then later menacingly stands over Stark, or is that some sort of dream sequence I wonder.

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The going theory I think is that, similar to a plot-line in the comics, the suit gains its own consciousness. Probably due to whatever "Extremis"-like experiments Stark is conducting on it in order to better don and use the suit.

-Thrown out of a window
-Going into space on low power
-Nearly chopped up by the helicarriers turbine blades
-He was so sure that he wouldn't make it back from delivering the nuke he tried to call Pepper.

It's possible that Stark synched his brain waves to the new armor.

When he has nightmares his subconscious activates the armor. Stark's priority to "Protect" leaks into the armor

I like that they're not shying away from negative consequences of that battle. And for someone like Tony, it makes sense to suffer from PTSD after something like this.
He's no soldier after all.
Cap fought on the frontlines in WW II. Widow and Hawkeye fought in modern battles (judging from the Budapest footage or whatever that was).
Thor? Please, he's seen thousands of battles over the eons.
They're all used to this shit as opposed to Tony.